Fruit quality and taste are important traits in the production of food crops. The taste of ripe tomato fruit is predominantly determined by sugar and titratable acid content, jointly measured in degrees Brix. Brix level is determined by environmental and genetic factors. Although alleles that increase Brix levels in tomato fruit have been identified in non-cultivated plant lines, efforts to introduce these alleles into cultivated lines have been hindered horticultural deficiencies. With any trait introgression from a wild relative, it is unknown whether the often found horticultural deficiencies are the result of pleiotropy, or due to by linkage drag. Linkage drag results from tightly associated genes near the gene of interest. Overcoming linkage drag is difficult, and a common hurdle to overcome is a lack recombination that would facilitate the separation of the genes causing drag, from the beneficial locus. Commonly, recombination can be suppressed in genomic regions introgressed from non-cultivated, wild relative species of a crop plant. The use of marker-assisted selection (MAS) in plant breeding methods has made it possible to select plants based on genetic markers linked to traits of interest. However accurate markers for identifying or tracking desirable traits in plants are frequently unavailable even if a gene associated with the trait has been characterized. These difficulties are further complicated by factors such as epistasis and polygenic or quantitative inheritance, which often lead to an incomplete understanding of the genetic background underlying expression of a desired phenotype. Therefore, in the absence of accurate and validated markers for use in MAS, it may not be feasible to produce new plant lines exhibiting certain beneficial phenotypes.